The Trouble With Heritage
by Lyoko Shinobi
Summary: Naruto learns about his heritage at a young age. However it does not create a better life for him like he hoped. In fact it does the opposite, it sparks a civil war. AU Pairings to be decided later.
1. Discovery

**Yo! What is up guys? It has been an incredibly long time since I lasted posted on Fanfiction. I could give a lot of excuses, but I won't. Anyways this idea came to me while watching some old Naruto episodes. Without Further ado. Enjoy!**

**Disclaimer: I do not own Naruto.**

Ch. 1 Discovery

Umino Iruka did like teaching, really he did. This was his fourth year teaching and he had graduated dependable shinobi during that time; some of them hand even made chunin since graduating. And even now he had new students coming that were unlike anything he had ever seen in years past. That thought alone would motivate most instructors to put forth a graduating class that could potentially be hailed as the village's greatest. But there was one thing, or rather one person who Iruka was not looking forward to seeing. That was one Uzumaki Naruto. It wasn't that he disliked Naruto, rather that he disliked his antics and his constant slacking off in class.

Iruka sighed and walked down the hall towards his classroom. When he reached the door he sighed again and braced himself for the day ahead. When he entered the room began to slowly but steadily quiet down. Iruka shook his head on the inside knowing why his class was being extra well-behaved today. Today they were supposed to have class outside so that they could have some light spars and practice shuriken throwing. They may be training to become ninjas but at the end of the day they were still children.

Naruto held his breath waiting for his sensei to say the words he had been waiting for all morning. He really wanted to do some sparring, especially with Sasuke. He couldn't wait to beat Sasuke up and prove he was stronger. He didn't have anything against the Uchiha, except that he had the affection of a certain pink-haired kunoichi-to-be: Sakura Haruno. Naruto was determined to get her and like him but even more than that he wanted to be the strongest. Everyone kept saying Sasuke was the strongest, but Naruto had a dream of being Hokage. To be the Hokage, you have to be the strongest shinobi; everyone knew that.

"Let's go outside," Iruka said snapping Naruto out of his reverie.

Naruto cheered with his classmates and then rushed to the door. On his way out he knocked a textbook off of Iruka's desk. He paid it no mind and kept heading for the door.

"Naruto," Iruka called after him. "Come pick up this book you knocked down."

Naruto skidded to a halt before turning to see he did in fact knock the book down. Pouting, Naruto went to pick up the book. It had fallen open to the section about the Yondaime's battle with the nine-tailed fox. Naruto's eyes fell on the picture of the Yondaime himself.

"Namikaze Minato, also known as the Yellow Flash, defeated the Kyuubi no Yoko on October tenth. A battle in which he would give his life to save the village from certain destruction." Naruto read to himself.

"Hey, Iruka-sensei look. It says the Yondaime defeated the Kyuubi on my birthday. That's crazy isn't it?" Naruto asked with surprise.

"Actually no, it's not. The Yondaime sealed the Kyuubi inside of you on the day you were born. But why he chose you, I do not know," Iruka thought.

Iruka moved to look at the book over Naruto's shoulder. He had read this section of the book a thousand times, but now there was something about this passage that he could not place. But what was it?

"Yeah, what a coincidence. Go on ahead Naruto, I'll be there in a minute," Iruka told him.

Naruto set the book down and turned and dashed outside not noticing that Iruka was intently going over the passage Naruto had indicated.

"Why did you pick Naruto, Yondaime? What set him apart from the other children? What made you decide to choose him? Did you see something in him?" Iruka wondered.

After a few minutes of this passed, Mizuki stepped into the classroom.

"Iruka, what are you doing? The kids are waiting for you," Mizuki said.

"Mizuki, come here for a minute," Iruka said not looking up.

A questioning look crossed Mizuki's face but he complied anyways. He looked over Iruka's shoulder at the text book.

"You're not planning on giving me a history lesson are you?" Mizuki half joked. "I know what happened that day. I was there and you were too."

"Yes, but have you noticed that the Yondaime and Naruto look similar?" Iruka asked.

"You're right; they look similar. But what does that matter? So they look alike. Big deal," Mizuki said not caring in the least. To him the boy was still the fox reincarnate.

"And the fox was sealed when Naruto was born. But why did the Yondaime choose Naruto? How could he choose to do that to a newborn?" Iruka asked now thoroughly confused by his former leader's actions.

"It's not like anybody missed him. Naruto's parents were killed that day by the Kyuubi," Mizuki replied.

Just then the object of their musings poked his head in the doorway.

"Iruka-sensei, Mizuki-sensei what's taking so long?" Naruto whined.

Iruka turned to Naruto. Yes, it was undeniable. The resemblance was definitely there. But he still wasn't a hundred percent of his hunch. He needed one more piece of evidence before he confronted the Hokage about it.  
"Naruto, what did Hokage-sama tell you about your father?" Iruka asked.

"He didn't say much. He told me he died in the battle against the Kyuubi and that he was one of the strongest shinobi of all time," Naruto said rather proudly.

Iruka nodded trying his hardest to hide his expression from the boy, which was a mix of awe and sorrow towards who he know knew was the late Yondaime's son. Mizuki narrowed his eyes as he also reached the same conclusion as his fellow chuunin. A lot of shinobi were killed in the battle against the Kyuubi but only one of them could be called one of the strongest of all time, and that was the Yondaime himself. This new information was interesting. But he refused to see this brat as anything more than the fox reincarnate. Nevertheless, he knew some would be foolish enough to believe he was not a demon but in fact the son of their hero.

Naruto looked at his teachers with a confused expression on his face. After he told them what old man Hokage said they got these funny looks on their face. Suddenly Mizuki stalked past Naruto and left. Even more confused Naruto turned to his other teacher.

"Naruto tell the other students that class is dismissed for today," Iruka said before following after Mizuki.

Naruto didn't even bother to try to understand what just happened. He did know that class was out early and it would give him more time to go play. A grin appeared on his face before he ran to tell his class the good news.

"Mizuki, wait," Iruka called after his friend. "We need to talk to the Hokage about what we have discovered."

"Of course, what did you think I was going to do?" Mizuki agreed. "Although, it is late. Hokage-sama is probably busy right now. Maybe we should just wait until tomorrow to tell him."

"Good idea, but I wonder why he kept it a secret. If he told everyone it would have saved Naruto a lot of pain." Iruka wondered aloud.

"I don't know, but I have to go now. I have something important to do. So I'll meet you here to tomorrow afternoon and we'll visit with Hokage-sama." Mizuki said before hastily taking his leave.

Iruka, deep in thought, merely nodded and did not think much of his friend's strange behavior. He was still thinking about what he had learned and how they would confront the Hokage about what they had discovered. But more importantly how this revelation would affect Naruto as well as the village itself.

**There you have it. I really like this idea and I am open to any and all suggestions because of the sheer possibility of this story. I will try to update in a timely manner. But I am in the midst of writing a novel, a joint story with some friends and college so cut me some slack. In the mean time please review and let me know what you guys think.**


	2. Not Alone Anymore

**And I'm back with another chapter after just a week. C'mon admit you're impressed... Well I'm impressed with myself. Without further ado. Enjoy!**

**Disclaimer: I don't own Naruto.**

Ch. 2 Not Alone Anymore

Mizuki hurriedly made his way back to the training fields near the edge of the village. With what he now knew he needed to tell his master Orochimaru about this new development. But he knew that was impossible so he settled for the next best thing: telling Kabuto, Orochimaru's second in command.

Kabuto often was near the training fields so as to avoid being seen in public. Because of this Mizuki did not trust him, and was always wary of him. Kabuto had the rank of genin, but as the right hand man of Orochimaru surely he was at a higher level. What that level was he did not know, and every time he tried to find out all the reports said that he was weak and got injured often on missions, adding more to Mizuki's distrust of him. When Mizuki arrived at the training fields Kabuto was nowhere to be found.

"Kabuto, show yourself!" Mizuki called out after a while of searching. "I've learned something important that could prove useful to Orochimaru-sama."

"Do not speak so lightly of Orochimaru. Your service to him is a on a trial basis only. Until you prove your worth, you are not even good enough to be called his pawn," Kabuto said appearing before the chuunin.

"Come now Kabuto, let us at least listen to what Mizuki-san has to say," a voice reminiscent of a snake said.

Orochimaru stepped out from behind the now terrified chuunin. The snake sannin smirked at Mizuki's reaction.

"Now speak quickly, I have some business I must attend to before I leave this place," Orochimaru commanded.

"Hai, Orochimaru-sama," Mizuki said snapping out of his fear-induced stupor. "Earlier today I learned something interesting about the demon brat, Naruto. It seems that he is the son of the late Yondaime."

Orochimaru's eyes widened. If what Mizuki said was true than this child had unlimited potential. To inherit the large chakra capacities from both Minato and Kushina, could result in a chakra pool rivaling that of a tailed-beast by the time the boy was a teenager. Add in the vitality of the Uzumaki clan and these two factors alone would make for an incredibly powerful shinobi. But it didn't end there both Minato and Kushina were masters at fuinjutsu and the child would have access to all this knowledge that had been locked away in the Namikaze estate. And to top it off the boy held the Kyubi no Yoko inside of him.

Orochimaru shuddered at the amount of power this boy had the potential for, though it was not in fear. If he could find a way to make that power work for him he would become unstoppable and he had just the jutsu for such an occasion.

"However that jutsu is still imperfect, but no matter I will wait and allow the boy time to grow in power before I steal it for my own. By then, I will have the jutsu ready for use," Orochimaru thought with satisfaction.

Orochimaru turned his attention back to the visibly shaking chuunin. "You have done well, but now I have one more task for you."

"Hai, whatever this task is I will not fail," Mizuki said a little confidence returning to him.

"Very good. Now I want you to kill Naruto. Then you are to leave the village and await further instructions at our nearest base," Orochimaru ordered.

Mizuki was confused by this order but he was not brave enough to question it. He hurriedly left after murmuring his assent to the orders given.

"Why do you want him to kill Naruto?" Kabuto asked. "Isn't he required for Akatsuki's plans to work?"

"Mizuki will not succeed, in fact he will die trying, and you are to make sure he does," Orochimaru said pointedly. "As for Akatsuki, do not believe that my plans are the same as theirs. For now they are simply a means to end. This cloak I wear is simply a way to gain power and to learn about what they have planned in the future."

"I see, and do you know what their plans are?" Kabuto asked.

"Only that it involves all the jinchuuriki. But I need you to look into another matter for me. The leader of Akatsuki goes by the name of Pein. He possesses the legendary Rinnegan. Find out what you can about the Rinnegan and Pein."

Kabuto nodded. He had heard of this person before but never more than in passing and it was always in fear of his power. Just how powerful was the Rinnegan?

"I have one more task I would like you to do," Orochimaru added. "I want you to share with the villagers what we have learned from Mizuki-kun. I think they would be interested to learn that their own jinchuuriki is also the son of their hero the Yondaime. I advise you move quickly, Mizuki will surely move quickly to try and take the boy's life."

Kabuto did not understand the reasoning behind Orochimaru's second request but he did not question it. He nodded and vanished to set about his tasks. Orochimaru chuckled to himself. Konoha would soon be in chaos and when the time was right he would move and take control of the village. And then he would have both Naruto and the Sharingan. Nothing would be able to stand in his way.

Mizuki was moving very quickly through the streets. He hated everything about Naruto, and now he was given the opportunity to off him himself. Despite Mizuki's uncharacteristic excitement he knew he had to be careful about how he went about taking care of Naruto. But first he needed to find the orange wearing jinchuuriki.

Mizuki came to a halt. The truth was he had absolutely no idea where to find Naruto. In his hatred of the boy he had learned next to nothing about him so he had nothing to go off of. Then he saw the key to finding Naruto. Iruka. He was friendly with the boy; surely he knew where to find something.

"Yo, Iruka," Mizuki called out.

Iruka stopped and turned to see his friend approaching him. "Ah, Mizuki what are you doing out here?"

"I was looking for Naruto. I have something to tell him," Mizuki added quickly.

"You're not going to tell him what we found out are you?" Iruka asked. "We should speak with Hokage-sama first."

"No, Naruto had uh…asked a question about taijutsu. And I wanted to tell him the answer," Mizuki lied.

"Well he might be at Ichiraku, but couldn't his question wait until tomorrow?" Iruka's words fell on deaf ears as Mizuki had run off in the middle of his sentence.

Iruka was bewildered by what just had happened. Since when was Mizuki eager to help Naruto? Iruka knew something was amiss and followed after his fellow chuunin in the direction of the ramen stand.

When he neared the stand he saw Mizuki speaking to Naruto. Iruka couldn't hear what was being said but shortly after Naruto left with Mizuki after downing his what seemed to be his sixth bowl of ramen. Iruka took a moment to shake his head at Naruto's unhealthy eating habits before following the now retreating forms of Mizuki and Naruto. After a few minutes Iruka realized that Mizuki was leading Naruto to a more secluded part of the village, where there were hardly any buildings and it was mainly trees. The two began to talk for a few minutes and for a moment Iruka thought that maybe Mizuki had been telling the truth. Iruka was about leave when Mizuki raised his voice to almost a shout.

"Don't try to act innocent with me! You are the Kyuubi no Yoko and you dare to masquerade as the Yondaime's son! I will do this world a favor and kill you!" Mizuki shouted.

Mizuki pulled out a kunai from his holster and in a single motion brought it slashing down towards Naruto. Naruto had no time to react; he was surely going to die. He would never become Hokage, he would never get Sakura to love him back and he would never have any friends. Naruto closed his eyes, his tears betraying him for the first time in years.

Naruto never felt the deathblow. He opened his eyes and saw Iruka had stopped the kunai with his own. Stunned, Naruto stumbled backwards and fell down.

"Mizuki what they hell are you doing?!" Iruka asked angrily though he already knew the answer.

"I'm doing what should have been done the year it was born. I'm killing that demon brat," Mizuki said. "And if you get in my way, I'll kill you too."

Mizuki brought his knee up into Iruka's gut forcing the air from his lungs. With his free hand Iruka blocked a punch from Mizuki, and pushed out of their deadlock. Iruka was panting, trying to replenish the oxygen in his lungs but Mizuki was being relentless. After several bouts of blocking Mizuki's attacks and being driven back Iruka saw an opening. Without thinking Iruka stabbed his kunai at Mizuki's exposed chest. Suddenly Mizuki brought his kunai inside of Iruka's thrust and forced his attack away before stabbing at Iruka's now fully exposed chest.

"There's no time. I can't stop him," Iruka realized with wide eyes.

Naruto stared horrified as he watched his sensei collapse. Was this what being a shinobi was like? Mizuki didn't even seem to care as he killed his "friend".

"Well someone will probably have heard something by now, so I'll just dispose of you quickly," Mizuki said his expression full of hate.

Mizuki pulled out three kunai with exploding tags attached to each of them. Mizuki looked directly at Naruto. He wanted to see the expression on the demon brat before it died. Naruto's expression was one of pure terror. Mizuki scoffed. Demons were not capable of feeling fear.

Mizuki lazily tossed his kunai at the boy. Naruto made no move to avoid the incoming explosives. A satisfied smirk crossed Mizuki's face when he saw movement beside him. Something blurred past him and threw itself in front of Naruto just before the explosion. The force of the explosion threw the two figures in separate directions. Mizuki frowned. Naruto was mostly unharmed save for a few scratches. But who protected him? Both Naruto and Mizuki looked at the other figure. It was Iruka. Mizuki was shocked. How had Iruka moved so fast with that injury?

Naruto rushed over to his fallen sensei. Iruka was badly burned from the explosion.

"Iruka-sensei, why? Why did you protect me?" Naruto asked.

"Because we're a lot alike. I know what it's like to be alone. I also know you're not a monster. You're a hero, just like your father. I should have been there more for you. I'm sorry," Iruka said in between violent fits of coughing.

"You don't have to apologize. It's my fault you go hurt," Naruto pleaded.

"Thank you, for letting me be a friend to you even if it was only for a short time," Iruka said before his eyes closed.

There was no stopping Naruto's tears now. He finally had a friend and he died because of him. Because he was too weak.

Mizuki burst into laughter. "What a fool. To save the monster that killed his parents. He's more of an idiot than I thought."

Something in Naruto broke. There was no holding back anymore. He felt a pulsation throughout his body and he was hit with two feelings he had never felt before. Rage and hate.

"I will kill you."

"The Sandaime said he would make an official decision by the week's end regarding the Uchiha," Itachi said to the masked man he was speaking to.

"Good, when the time comes I will help you kill them all," the masked man replied.

"Do not forget Madara, my brother is to be spared," Itachi reminded him calmly.

Madara waved his agreement. Itachi narrowed his eyes. Something was bothering the ancient Uchiha, or rather something else was grabbing his attention. Whatever it was, it was mostly likely important.

"As I thought, things have been accelerated greatly," Madara said after a while. "We cannot wait for the Sarutobi-san to make the decision. The village will soon be in an uproar."

"What makes you say that?" Itachi asked.

"It seems one of Orochimaru's minions has pushed Naruto too far," Madara said matter-of-factly.

Then it hit Itachi, a malignant chakra he had only felt once before eight years ago. It was surely the Kyuubi's chakra.

"Go stop Naruto. I don't know what has happened to Naruto, but this event will surely cause a panic amongst the villagers and possibly even the shinobi populace. But no matter what, side with Naruto. We still need him for Akatsuki's plans. Do what is necessary to protect him," Madara said before vanishing.

If Itachi was confused it didn't show, though there was no one to see even if he was. Itachi dashed in the direction of the chakra. Itachi knew that the Kyuubi was a creature of hate. So whatever caused the Kyuubi's chakra to leak out of Naruto was probably the result of intense anger by Naruto. This time confusion was evident on Itachi's face. All the times he had seen Naruto he always seemed so cheerful.

Naruto came into view. The blonde was straddling a body, who Itachi recognized as Mizuki, or what was left of him. Naruto was engulfed in a red chakra that took the form of a fox around him and the chuunin's skull was crushed and his chest was caved in. And Naruto was still punching the chuunin yelling out incoherently. Itachi didn't know what surprised him more, Naruto's appearance or a Mizuki's. Itachi moved to face Naruto who was still beating the corpse of Mizuki.

"Naruto let it go. He's dead," Itachi said softly.

Naruto paused only a moment to look at Itachi but he did not stop. Itachi was surprised to see tears streaming from the boy' eyes, though they kept evaporating from the heat of the chakra cloak. Itachi felt pity for the eight year old. What could have possibly pushed him to this point. Itachi activated his Sharingan.

"Naruto, stop. It's enough," Itachi said making eye contact.

Naruto instantly calmed down and the chakra cloak dissipated. But Naruto's tears did not stop. Itachi placed a hand on the boy's shoulder.

"It's ok."

"No, it's not. He killed him. He was my only friend," Naruto said instinctively placing his arms around Itachi as he cried into the Uchiha's shoulder.

Itachi, not knowing how to react, tentatively patted Naruto on the back. Itachi looked over Naruto's head and for the first time noticed Iruka's body. His Sharingan still activated he detected the smallest of chakra signatures.

"Do not worry Naruto, you will not be alone anymore. I promise you that," Itachi said reassuringly.

Itachi was not sure why he made that promise to this boy he barely knew but he did not want to take it back.

**There you go. A new chapter in a week not to mention that it's much longer than last chapter. I'd say that's worth a review. So please review, it's great motivation to keep writing. Sides will be chosen for the civil war next chapter. Once again let me know if you have any ideas and review!**


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